Project C: Systems Genetics of Metabolism; Ron Korstanje (Jackson) The mouse has been used as a model for many metabolic traits. Hundreds of QTL studies have been published. However, most of these studies measure single traits, even though clear correlations and interactions exist for multiple traits. In addition, these studies usually do not look at epigenetic or environmental effects. In a systems genetics approach to metabolic traits, with an emphasis on HDL cholesterol levels, we combine metabolic profiling, sequencing of RNA transcripts (RNAseq), whole-genome methylation mapping, and the mapping power of intercrossed recombinant inbred (RIX) Collaborative Cross (CC) mice to map metabolic syndrome related traits, liver (allele-specific) transcripts and splice variants and their interactions, on both a standard chow diet and a vitamin D enriched diet.